To What Extent are “Atoms in Molecules” Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

The “atoms in molecules” structures of 225 unsubstituted hydrocarbons are derived from both the optimized and the promolecule electron densities. A comparative analysis demonstrates that the molecular graphs derived from these two types of electron densities at the same geometry are equivalent for almost 90 % of the hydrocarbons containing the same number and types of critical points. For the remaining 10 % of molecules, it is demonstrated that by inducing small perturbations, through the variation of the used basis set or slight changes in the used geometry, the emerging molecular graphs from both densities are also equivalent. Interestingly, the (3, ?1) critical point between two “non‐bonded” hydrogen atoms, which triggered “H?H bonding” controversy is also observed in the promolecule densities of certain hydrocarbons. Evidently, the topology of the electron density is not dictated by chemical bonds or strong interactions and deformations induced by the interactions of atoms in molecules have a quite marginal role, virtually null, in shaping the general traits of the topology of molecular electron densities of the studied hydrocarbons, whereas the key factor is the underlying atomic densities.     

Muon‐Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution

Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014 , 53, 13706–13709; Angew. Chem. 2014, 126, 13925–13929 ] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear‐electronic orbital non‐Born–Oppenheimer procedure, the nuclear configuration of the muon‐substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the “atoms in molecules” (AIM) structure of the muon‐substituted malonaldehyde and the AIM structure of the stable and the transition‐state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon‐substituted malonaldehyde to the transition state.     

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds,Interactions, and Bond/Line Paths

Currently, bonding analysis of molecules based on the Quantum Theory of Atoms in Molecules (QTAIM) is popular; however, “misinterpretations” of the QTAIM analysis are also very frequent. In this contribution the chemical relevance of the bond path as one of the key topological entities emerging from the QTAIM’s topological analysis of the one‐electron density is reconsidered. The role of nuclear vibrations on the topological analysis is investigated demonstrating that the bond paths are not indicators of chemical bonds. Also, it is argued that the detection of the bond paths is not necessary for the “interaction” to be present between two atoms in a molecule. The conceptual disentanglement of chemical bonds/interactions from the bonds paths, which are alternatively termed “line paths” in this contribution, dismisses many superficial inconsistencies. Such inconsistencies emerge from the presence/absence of the line paths in places of a molecule in which chemical intuition or alternative bonding analysis does not support the presence/absence of a chemical bond. Moreover, computational QTAIM studies have been performed on some “problematic” molecules, which were considered previously by other authors, and the role of nuclear vibrations on presence/absence of the line paths is studied demonstrating that a bonding pattern consistent with other theoretical schemes appears after a careful QTAIM analysis and a new “interpretation” of data is performed.     

硼原子的键合形式对硼酸盐晶体非线性光学行为的影响

在几种具有典型复杂结构的硼酸盐晶体中 ,从硼原子的键合形式出发讨论了不同键合情况下的B—O键对硼酸盐晶体的非线性光学行为的具体影响。结果表明 ,晶体中B—O键的键合形式是制约硼酸盐晶体非线性光学行为的重要因素。     

Temperature‐Dependent Prediction of the Liquid Entropy of Ionic Liquids

Modeling of the temperature‐dependent liquid entropy of ionic liquids (ILs) with great accuracy using COSMO‐RS is demonstrated. The minimum structures of eight IL ion pairs are investigated and the entropy, calculated from ion pairs, is found to differ on average only 2 % from the available experimental values (119 data points). For calculations with single ions, the average error amounts to 2.6 % and stronger‐coordinating ions tend to give higher deviations. Additionally, the first parameterization of the standard liquid entropy for ILs is presented in the context of traditional volume‐based thermodynamics (S_l⁰=1.585 kJ mol^?1 K^?1 nm^?3?r_m³+14.09 J mol^?1 K^?1), which sheds light on the statistical treatment of ionic interactions. The findings provide the first direct access to accurate predictions of liquid entropies of ILs, which are tedious and time‐consuming to measure.     

Single electron densities: a new tool to analyze molecular wavefunctions

A new partitioning scheme for the electron density of a many-electron wavefunction into single electron densities is proposed. These densities are based on the most probable arrangement of the electrons in an atom or molecule. Therefore, they contain information about the electron-electron interaction and, most notably, the Fermi hole due to the antisymmetry of the many-electron wavefunction. The single electron densities overlap and can be combined to electron pair distributions close to the qualitative electron pairs that represent, for instance, the basis of the valence shell electron pair repulsion model. Single electron analyses are presented for the water, ethane, and ethene molecules. The effect of electron correlation on the single electron and pair densities is investigated for the water molecule.     

Polymorph Identification and Crystal Structure Determination by a Combined Crystal Structure Prediction and Transmission Electron Microscopy Approach

Electron diffraction offers advantages over X‐ray based methods for crystal structure determination because it can be applied to sub‐micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo‐inositol and theophylline.     

Bonding Trends in Molecular Compounds of Lanthanides: The Double‐Bonded Carbene Cations LnCH2+ (Ln=Sc,Y, La–Lu)

Quasi‐relativistic Douglas–Kroll CASPT2 calculations are reported for the title molecules, mainly to provide primary data for a fit of double‐bond covalent radii. Indeed, a well‐developed σ²π² double bond is identified in all cases. For Eu and Yb, however, it is an excited state. The main valence orbitals of all Ln ions are 6s and 5d. In the σ bonds, more 5d than 6s character is found at the Ln. The Ln?C bond lengths show a systematic lanthanide contraction of 13 pm from La to Lu. An agostic symmetry breaking is demonstrated for Ce but its effect on the Ln? C length is small.     

Determination of the Crystal Structure of a New Polymorph of Theophylline

A new approach to crystal structure determination, combining crystal structure prediction and transmission electron microscopy, was used to identify a potential new crystal phase of the pharmaceutical compound theophylline. The crystal structure was determined despite the new polymorph occurring as a minor component in a mixture with Form II of theophylline, at a concentration below the limits of detection of analytical methods routinely used for pharmaceutical characterisation. Detection and characterisation of crystallites of this new form were achieved with transmission electron microscopy, exploiting the combination of high magnification imaging and electron diffraction measurements. A plausible crystal structure was identified by indexing experimental electron‐diffraction patterns from a single crystallite of the new polymorph against a reference set of putative crystal structures of theophylline generated by global lattice energy minimisation calculations.     

Valence Bond and Enzyme Catalysis: A Time To Break Down and a Time To Build Up

Understanding enzyme catalysis and developing ability to control of it are two great challenges in biochemistry. A few successful examples of computational‐based enzyme design have proved the fantastic potential of computational approaches in this field, however, relatively modest rate enhancements have been reported and the further development of complementary methods is still required. Herein we propose a conceptually simple scheme to identify the specific role that each residue plays in catalysis. The scheme is based on a breakdown of the total catalytic effect into contributions of individual protein residues, which are further decomposed into chemically interpretable components by using valence bond theory. The scheme is shown to shed light on the origin of catalysis in wild‐type haloalkane dehalogenase (wt‐DhlA) and its mutants. Furthermore, the understanding gained through our scheme is shown to have great potential in facilitating the selection of non‐optimal sites for catalysis and suggesting effective mutations to enhance the enzymatic rate.     

A relation between energies of the short-lived negative ion states and energies of unfilled molecular orbitals for a series of bromoalkanes

A series of bromoalkanes was investigated by means of electron transmission spectroscopy in the gas phase. Experimental values of vertical electron affinities associated with occupation of the LUMO by an incoming electron were assigned using ab initio quantum chemical calculations. The predicted vertical electron affinity values differ from measured ones by at most ±0.2 eV. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1222–1224, June, 2007.     

The Electronic Structures and Chemical Bonding of Some Dinuclear and Trinuclear Low－valence Molybdenum Complexes Containing Thiolate Bridges

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High-pressure structural trends of Group 15 elements: simple packed structures versus complex host-guest arrangements

The Group 15 elements P, As, Sb, and Bi all have layered structures consisting of six-membered rings under ambient conditions and attain the body-centered cubic (bcc) structure at the highest pressures applied. In the intermediate pressure region, however, phosphorus and its heavier congeners behave profoundly differently. In this region P first attains the open packed simple cubic (sc) structure for a wide range of pressures and then transforms into the rarely observed simple hexagonal (sh) structure. For the heavier congeners complex, incommensurately modulated host-guest structures emerge as intermediate pressure structures. We investigated the high-pressure behavior of P and As by ab initio density functional calculations in which pseudopotentials and a plane wave basis set were employed. The incommensurately modulated high-pressure structure of As was approximated by a supercell. Our calculations reproduced the experimentally established pressure stability ranges of the sc and sh structures for P and the host-guest structure for As very well. We found that the sc and especially the sh structure are decisively stabilized by the admixture of d states in the occupied levels of the electronic structure. This admixture releases s-s antibonding states above the Fermi level (s-d mixing). With pressure, s-d mixing increases rapidly for P, whereas it remains at a low level for As. As a consequence, the band energy contribution to the total energy determines the structural stability for P in the intermediate pressure region, giving rise to simple packed structures. On the other hand, in the intermediate pressure region of the heavier Group 15 elements, a delicate interplay between the electrostatic Madelung energy and the band energy leads to the formation of complex structures.     

Modeling the IR Spectra of Aqueous Metal Carboxylate Complexes: Correlation between Bonding Geometry and Stretching Mode Wavenumber Shifts

A widely used principle is that shifts in the wavenumber of carboxylate stretching modes upon bonding with a metal center can be used to infer if the geometry of the bonding is monodentate or bidentate. We have tested this principle with ab initio modeling for aqueous metal carboxylate complexes and have shown that it does indeed hold. Modeling of the bonding of acetate and formate in aqueous solution to a range of cations was used to predict the infrared spectra of the metal‐carboxylate complexes, and the wavenumbers of the symmetric and antisymmetric vibrational modes are reported. Furthermore, we have shown that these shifts in wavenumber occur primarily due to how bonding with the metal changes the carboxylate C?O bond lengths and O‐C‐O angle.     

Different Catalytic Effects of a Single Water Molecule: The Gas‐Phase Reaction of Formic Acid with Hydroxyl Radical in Water Vapor

The effect of a single water molecule on the reaction mechanism of the gas‐phase reaction between formic acid and the hydroxyl radical was investigated with high‐level quantum mechanical calculations using DFT–B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6‐311+G(2df,2p) and aug‐cc‐pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton‐coupled electron transfer process (pcet), two hydrogen‐atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).     

Charge decomposition analysis of the electron localizability indicator: a bridge between the orbital and direct space representation of the chemical bond

The novel functional electron localizability indicator is a useful tool for investigating chemical bonding in molecules and solids. In contrast to the traditional electron localization function (ELF), the electron localizability indicator is shown to be exactly decomposable into partial orbital contributions even though it displays at the single-determinantal level of theory the same topology as the ELF. This approach is generally valid for molecules and crystals at either the single-determinantal or the explicitly correlated level of theory. The advantages of the new approach are illustrated for the argon atom, homonuclear dimers N2 and F2, unsaturated hydrocarbons C2H4 and C6H6, and the transition-metal-containing molecules Sc(2)2+ and TiF4.     

Vibrational Dephasing in Ionic Liquids as a Signature of Hydrogen Bonding

Understanding both structure and dynamics is crucial for producing tailor‐made ionic liquids (ILs). We studied the vibrational and structural dynamics of medium versus weakly hydrogen‐bonded C?H groups of the imidazolium ring in ILs of the type [1‐alkyl‐3‐methylimidazolium][bis(trifluoromethanesulfonyl)imide] ([C_nmim][NTf₂]), with n=1, 2, and 8, by time‐resolved coherent anti‐Stokes Raman scattering (CARS) and quantum‐classical hybrid (QCH) simulations. From the time series of the CARS spectra, dephasing times were extracted by modeling the full nonlinear response. From the QCH calculations, pure dephasing times were obtained by analyzing the distribution of transition frequencies. Experiments and calculations reveal larger dephasing rates for the vibrational stretching modes of C(2)?H compared with the more weakly hydrogen‐bonded C(4,5)?H. This finding can be understood in terms of different H‐bonding motifs and the fast interconversion between them. Differences in population relaxation rates are attributed to Fermi resonance interactions.